Cycles bake to a flat surface / plane
Okay so I've prepared this blend file: http://www.pasteall.org/blend/40069

It's a crude attempt at recreating your scene, but essentially, we have a large plane (which we want to bake our geometry to), and a number of smaller planes (which represents the geometry you want to bake)

Open the file. Select the large plane, tab into edit mode, select all vertices, press U, and then select "Unwrap"

Right click on the edge of the 3D viewport, select "Split area", and in the new area that appears, switch to the UV image editor. In the UV image editor, select "New" from the toolbar along the bottom, and create a new image:



Next, in the materials tab, create a new material, and under the "Surface" panel, click the little dot to the right of the "Color" widget, and select "Image Texture":



Click the dropdown to the left of the "Open" button, and select the image that you created in the UV image editor. Next, tab out of edit mode, and back into object mode. In the 3D viewport, select all the smaller planes, and then select the large plane. Make sure you select the large plane last, as this will make it the active object in the scene (indicated by the brighter shader of orange):



Next, under the Render tab, scroll down to the Bake panel, change the Bake type to "Diffuse Color", check "Selected to Active", and set the margin to 0px, and click "Bake":



Now, in the UV image editor pane, you should see the geometry of your scene baked onto the texture. However, you will notice that only some of the geometry has been baked to the plane, which I think is what's happening in your first screenshot. To capture the remaining geometry, increase the "Ray Distance" value under the "Bake" panel (it's located just under the "Selected to Active" checkbox). In my example, I have set "Ray Distance" to 3. Now, click "Bake" again, and this time, all geometry will be captured in the bake:



Does that solve your problem?